data_4K42 # _model_server_result.job_id SlBnKT01zjk0_nbvrTspxg _model_server_result.datetime_utc '2024-11-24 20:37:07' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4k42 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 4K42 # _exptl.entry_id 4K42 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.42 _cell.angle_gamma 90 _cell.entry_id 4K42 _cell.length_a 54.65 _cell.length_b 67.343 _cell.length_c 207.853 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4K42 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G,Q 1 1 B,H,I,J,R 2 1 C,K,L,M,S 3 1 D,N,O,P,T 4 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 I N N ? 3 L N N ? 3 O N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 E CA CA . A CA 401 1_555 F O2B ADP . A ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc2 E CA CA . A CA 401 1_555 Q O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc3 E CA CA . A CA 401 1_555 Q O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc4 K CA CA . C CA 401 1_555 L O3B ADP . C ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc5 K CA CA . C CA 401 1_555 L O2B ADP . C ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.122 ? metalc ? metalc6 N CA CA . D CA 401 1_555 O O3B ADP . D ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? metalc ? metalc7 N CA CA . D CA 401 1_555 O O2B ADP . D ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? metalc ? metalc8 N CA CA . D CA 401 1_555 T O HOH . D HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 4K42 _atom_sites.fract_transf_matrix[1][1] 0.018298 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000775 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014849 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.004815 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code E 2 CA A 1 401 376 CA CA . F 3 ADP A 1 402 380 ADP ADP . G 4 NWM A 1 403 381 NWM NWM . H 2 CA B 1 401 376 CA CA . I 3 ADP B 1 402 380 ADP ADP . J 4 NWM B 1 403 381 NWM NWM . K 2 CA C 1 401 376 CA CA . L 3 ADP C 1 402 380 ADP ADP . M 4 NWM C 1 403 381 NWM NWM . N 2 CA D 1 401 376 CA CA . O 3 ADP D 1 402 380 ADP ADP . P 4 NWM D 1 403 381 NWM NWM . Q 5 HOH A 1 501 8 HOH HOH . Q 5 HOH A 2 502 9 HOH HOH . Q 5 HOH A 3 503 15 HOH HOH . Q 5 HOH A 4 504 19 HOH HOH . Q 5 HOH A 5 505 21 HOH HOH . Q 5 HOH A 6 506 25 HOH HOH . Q 5 HOH A 7 507 29 HOH HOH . Q 5 HOH A 8 508 30 HOH HOH . Q 5 HOH A 9 509 34 HOH HOH . Q 5 HOH A 10 510 35 HOH HOH . Q 5 HOH A 11 511 37 HOH HOH . Q 5 HOH A 12 512 42 HOH HOH . Q 5 HOH A 13 513 43 HOH HOH . Q 5 HOH A 14 514 44 HOH HOH . Q 5 HOH A 15 515 46 HOH HOH . Q 5 HOH A 16 516 49 HOH HOH . Q 5 HOH A 17 517 50 HOH HOH . Q 5 HOH A 18 518 52 HOH HOH . Q 5 HOH A 19 519 53 HOH HOH . Q 5 HOH A 20 520 54 HOH HOH . Q 5 HOH A 21 521 58 HOH HOH . Q 5 HOH A 22 522 59 HOH HOH . Q 5 HOH A 23 523 62 HOH HOH . Q 5 HOH A 24 524 65 HOH HOH . Q 5 HOH A 25 525 67 HOH HOH . Q 5 HOH A 26 526 68 HOH HOH . Q 5 HOH A 27 527 69 HOH HOH . Q 5 HOH A 28 528 74 HOH HOH . Q 5 HOH A 29 529 78 HOH HOH . Q 5 HOH A 30 530 79 HOH HOH . Q 5 HOH A 31 531 80 HOH HOH . Q 5 HOH A 32 532 83 HOH HOH . Q 5 HOH A 33 533 86 HOH HOH . Q 5 HOH A 34 534 87 HOH HOH . Q 5 HOH A 35 535 90 HOH HOH . Q 5 HOH A 36 536 91 HOH HOH . Q 5 HOH A 37 537 95 HOH HOH . Q 5 HOH A 38 538 97 HOH HOH . Q 5 HOH A 39 539 100 HOH HOH . Q 5 HOH A 40 540 101 HOH HOH . Q 5 HOH A 41 541 102 HOH HOH . Q 5 HOH A 42 542 104 HOH HOH . R 5 HOH B 1 501 5 HOH HOH . R 5 HOH B 2 502 6 HOH HOH . R 5 HOH B 3 503 7 HOH HOH . R 5 HOH B 4 504 16 HOH HOH . R 5 HOH B 5 505 20 HOH HOH . R 5 HOH B 6 506 26 HOH HOH . R 5 HOH B 7 507 27 HOH HOH . R 5 HOH B 8 508 38 HOH HOH . R 5 HOH B 9 509 51 HOH HOH . R 5 HOH B 10 510 56 HOH HOH . R 5 HOH B 11 511 60 HOH HOH . R 5 HOH B 12 512 81 HOH HOH . R 5 HOH B 13 513 84 HOH HOH . R 5 HOH B 14 514 89 HOH HOH . R 5 HOH B 15 515 96 HOH HOH . S 5 HOH C 1 501 1 HOH HOH . S 5 HOH C 2 502 2 HOH HOH . S 5 HOH C 3 503 4 HOH HOH . S 5 HOH C 4 504 10 HOH HOH . S 5 HOH C 5 505 12 HOH HOH . S 5 HOH C 6 506 17 HOH HOH . S 5 HOH C 7 507 22 HOH HOH . S 5 HOH C 8 508 23 HOH HOH . S 5 HOH C 9 509 28 HOH HOH . S 5 HOH C 10 510 31 HOH HOH . S 5 HOH C 11 511 32 HOH HOH . S 5 HOH C 12 512 36 HOH HOH . S 5 HOH C 13 513 39 HOH HOH . S 5 HOH C 14 514 40 HOH HOH . S 5 HOH C 15 515 41 HOH HOH . S 5 HOH C 16 516 47 HOH HOH . S 5 HOH C 17 517 48 HOH HOH . S 5 HOH C 18 518 55 HOH HOH . S 5 HOH C 19 519 57 HOH HOH . S 5 HOH C 20 520 61 HOH HOH . S 5 HOH C 21 521 63 HOH HOH . S 5 HOH C 22 522 64 HOH HOH . S 5 HOH C 23 523 70 HOH HOH . S 5 HOH C 24 524 71 HOH HOH . S 5 HOH C 25 525 72 HOH HOH . S 5 HOH C 26 526 73 HOH HOH . S 5 HOH C 27 527 75 HOH HOH . S 5 HOH C 28 528 76 HOH HOH . S 5 HOH C 29 529 82 HOH HOH . S 5 HOH C 30 530 85 HOH HOH . S 5 HOH C 31 531 88 HOH HOH . S 5 HOH C 32 532 92 HOH HOH . S 5 HOH C 33 533 93 HOH HOH . S 5 HOH C 34 534 98 HOH HOH . S 5 HOH C 35 535 105 HOH HOH . T 5 HOH D 1 501 3 HOH HOH . T 5 HOH D 2 502 11 HOH HOH . T 5 HOH D 3 503 13 HOH HOH . T 5 HOH D 4 504 14 HOH HOH . T 5 HOH D 5 505 18 HOH HOH . T 5 HOH D 6 506 24 HOH HOH . T 5 HOH D 7 507 33 HOH HOH . T 5 HOH D 8 508 66 HOH HOH . T 5 HOH D 9 509 77 HOH HOH . T 5 HOH D 10 510 94 HOH HOH . T 5 HOH D 11 511 99 HOH HOH . T 5 HOH D 12 512 103 HOH HOH . T 5 HOH D 13 513 106 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB ADP . . . F 3 -6.218 10.186 -85.852 1 44.01 ? PB ADP 402 A 1 HETATM 2 O O1B ADP . . . F 3 -7.561 10.637 -85.329 1 42.47 ? O1B ADP 402 A 1 HETATM 3 O O2B ADP . . . F 3 -5.292 9.667 -84.763 1 44.91 ? O2B ADP 402 A 1 HETATM 4 O O3B ADP . . . F 3 -5.594 11.145 -86.852 1 42.49 ? O3B ADP 402 A 1 HETATM 5 P PA ADP . . . F 3 -6.195 7.379 -86.209 1 48.07 ? PA ADP 402 A 1 HETATM 6 O O1A ADP . . . F 3 -4.701 7.152 -86.309 1 50.59 ? O1A ADP 402 A 1 HETATM 7 O O2A ADP . . . F 3 -6.915 7.164 -84.899 1 47.91 ? O2A ADP 402 A 1 HETATM 8 O O3A ADP . . . F 3 -6.519 8.873 -86.735 1 32.52 ? O3A ADP 402 A 1 HETATM 9 O O5' ADP . . . F 3 -6.919 6.55 -87.371 1 15.69 ? O5' ADP 402 A 1 HETATM 10 C C5' ADP . . . F 3 -8.329 6.383 -87.443 1 18.81 ? C5' ADP 402 A 1 HETATM 11 C C4' ADP . . . F 3 -8.657 6.113 -88.907 1 23.81 ? C4' ADP 402 A 1 HETATM 12 O O4' ADP . . . F 3 -8.048 4.88 -89.273 1 28.96 ? O4' ADP 402 A 1 HETATM 13 C C3' ADP . . . F 3 -10.139 5.983 -89.221 1 24.4 ? C3' ADP 402 A 1 HETATM 14 O O3' ADP . . . F 3 -10.427 6.706 -90.423 1 24.08 ? O3' ADP 402 A 1 HETATM 15 C C2' ADP . . . F 3 -10.386 4.503 -89.438 1 23.18 ? C2' ADP 402 A 1 HETATM 16 O O2' ADP . . . F 3 -11.385 4.235 -90.438 1 16.75 ? O2' ADP 402 A 1 HETATM 17 C C1' ADP . . . F 3 -9.011 4.015 -89.871 1 28.39 ? C1' ADP 402 A 1 HETATM 18 N N9 ADP . . . F 3 -8.754 2.613 -89.468 1 26.45 ? N9 ADP 402 A 1 HETATM 19 C C8 ADP . . . F 3 -8.676 2.139 -88.218 1 26.45 ? C8 ADP 402 A 1 HETATM 20 N N7 ADP . . . F 3 -8.42 0.806 -88.212 1 23.16 ? N7 ADP 402 A 1 HETATM 21 C C5 ADP . . . F 3 -8.325 0.424 -89.492 1 20.07 ? C5 ADP 402 A 1 HETATM 22 C C6 ADP . . . F 3 -8.083 -0.836 -90.206 1 20.92 ? C6 ADP 402 A 1 HETATM 23 N N6 ADP . . . F 3 -7.874 -1.994 -89.54 1 23.79 ? N6 ADP 402 A 1 HETATM 24 N N1 ADP . . . F 3 -8.06 -0.783 -91.549 1 20.94 ? N1 ADP 402 A 1 HETATM 25 C C2 ADP . . . F 3 -8.254 0.344 -92.25 1 20.78 ? C2 ADP 402 A 1 HETATM 26 N N3 ADP . . . F 3 -8.488 1.523 -91.66 1 20.49 ? N3 ADP 402 A 1 HETATM 27 C C4 ADP . . . F 3 -8.54 1.617 -90.315 1 21.97 ? C4 ADP 402 A 1 HETATM 28 H "H5'1" ADP . . . F 3 -8.838 7.287 -87.1 1 22.57 ? "H5'1" ADP 402 A 1 HETATM 29 H "H5'2" ADP . . . F 3 -8.645 5.543 -86.821 1 22.57 ? "H5'2" ADP 402 A 1 HETATM 30 H H4' ADP . . . F 3 -8.24 6.927 -89.515 1 28.57 ? H4' ADP 402 A 1 HETATM 31 H H3' ADP . . . F 3 -10.74 6.35 -88.377 1 29.28 ? H3' ADP 402 A 1 HETATM 32 H H2' ADP . . . F 3 -10.657 4.033 -88.482 1 27.81 ? H2' ADP 402 A 1 HETATM 33 H HO2' ADP . . . F 3 -12.23 4.616 -90.16 1 20.1 ? HO2' ADP 402 A 1 HETATM 34 H H1' ADP . . . F 3 -8.945 4.097 -90.965 1 34.07 ? H1' ADP 402 A 1 HETATM 35 H H8 ADP . . . F 3 -8.813 2.739 -87.327 1 31.74 ? H8 ADP 402 A 1 HETATM 36 H HN61 ADP . . . F 3 -7.698 -2.846 -90.052 1 28.54 ? HN61 ADP 402 A 1 HETATM 37 H HN62 ADP . . . F 3 -7.888 -2.005 -88.53 1 28.54 ? HN62 ADP 402 A 1 HETATM 38 H H2 ADP . . . F 3 -8.229 0.298 -93.331 1 24.93 ? H2 ADP 402 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 217 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 38 #